Starting phenix.real_space_refine
on Fri Oct 10 11:42:08 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8otj_17181/10_2025/8otj_17181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8otj_17181/10_2025/8otj_17181.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8otj_17181/10_2025/8otj_17181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8otj_17181/10_2025/8otj_17181.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8otj_17181/10_2025/8otj_17181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8otj_17181/10_2025/8otj_17181.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       7      5.16       5
     C    2569      2.51       5
     N     756      2.21       5
     O     777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4109
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 0.91, per 1000 atoms: 0.22
  Number of scatterers: 4109
  At special positions: 0
  Unit cell: (132.986, 108.206, 40.474, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       7     16.00
     O     777      8.00
     N     756      7.00
     C    2569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 173.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  938

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 48.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.251A  pdb=" N   VAL A 306 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   VAL B 309 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE A 308 " --> pdb=" O   VAL B 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 7.043A  pdb=" N   VAL A 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL E 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 324
      removed outlier: 6.303A  pdb=" N   VAL A 318 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   LYS B 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   SER A 320 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY B 323 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   CYS A 322 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   SER E 324 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   SER F 324 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.072A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.432A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 346
      removed outlier: 6.557A  pdb=" N   LEU A 344 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 359
      removed outlier: 6.342A  pdb=" N   VAL A 350 " --> pdb=" O   GLN B 351 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS B 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER A 352 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLY B 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   ILE A 354 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LEU B 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   SER A 356 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 10.592A  pdb=" N   ASN B 359 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 9.432A  pdb=" N   ASP A 358 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER E 356 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU A 357 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP E 358 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN A 359 " --> pdb=" O   ASP E 358 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER F 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU E 357 " --> pdb=" O   SER F 356 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP F 358 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN E 359 " --> pdb=" O   ASP F 358 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 373
      removed outlier: 6.366A  pdb=" N   ASN A 368 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE B 371 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LYS A 370 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   THR B 373 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU A 372 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 378 through 379
      removed outlier: 6.560A  pdb=" N   PHE A 378 " --> pdb=" O   ARG B 379 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.251A  pdb=" N   VAL C 306 " --> pdb=" O   GLN G 307 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   VAL G 309 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE C 308 " --> pdb=" O   VAL G 309 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 7.044A  pdb=" N   VAL C 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 324
      removed outlier: 6.802A  pdb=" N   SER D 324 " --> pdb=" O   GLY C 323 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL C 318 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   LYS G 321 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   SER C 320 " --> pdb=" O   LYS G 321 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY G 323 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.732A  pdb=" N   CYS C 322 " --> pdb=" O   GLY G 323 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330
      removed outlier: 6.073A  pdb=" N   ILE C 328 " --> pdb=" O   HIS G 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 340
      removed outlier: 6.431A  pdb=" N   VAL C 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   LYS G 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL C 339 " --> pdb=" O   LYS G 340 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 343 through 346
      removed outlier: 6.558A  pdb=" N   LEU C 344 " --> pdb=" O   ASP G 345 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 349 through 359
      removed outlier: 6.783A  pdb=" N   SER D 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU C 357 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP D 358 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN C 359 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL C 350 " --> pdb=" O   GLN G 351 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   LYS G 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER C 352 " --> pdb=" O   LYS G 353 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLY G 355 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE C 354 " --> pdb=" O   GLY G 355 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LEU G 357 " --> pdb=" O   ILE C 354 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   SER C 356 " --> pdb=" O   LEU G 357 " (cutoff:3.500A)
      removed outlier: 10.593A  pdb=" N   ASN G 359 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 9.431A  pdb=" N   ASP C 358 " --> pdb=" O   ASN G 359 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 368 through 373
      removed outlier: 6.365A  pdb=" N   ASN C 368 " --> pdb=" O   LYS G 369 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE G 371 " --> pdb=" O   ASN C 368 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LYS C 370 " --> pdb=" O   ILE G 371 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   THR G 373 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   GLU C 372 " --> pdb=" O   THR G 373 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 378 through 379
      removed outlier: 6.560A  pdb=" N   PHE C 378 " --> pdb=" O   ARG G 379 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    285 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.69

  Time building geometry restraints manager: 0.40 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1175
        1.34 -     1.46: 973
        1.46 -     1.58: 2017
        1.58 -     1.70: 0
        1.70 -     1.82: 7
  Bond restraints: 4172
  Sorted by residual:
  bond pdb=" C   LYS D 331 "
       pdb=" N   PRO D 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.364 -0.032 1.28e-02 6.10e+03 6.39e+00
  bond pdb=" C   LYS B 331 "
       pdb=" N   PRO B 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.364 -0.032 1.28e-02 6.10e+03 6.32e+00
  bond pdb=" C   LYS E 331 "
       pdb=" N   PRO E 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.28e-02 6.10e+03 6.24e+00
  bond pdb=" C   LYS G 331 "
       pdb=" N   PRO G 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.28e-02 6.10e+03 6.23e+00
  bond pdb=" C   LYS A 331 "
       pdb=" N   PRO A 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.28e-02 6.10e+03 6.21e+00
  ... (remaining 4167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 4244
        1.87 -     3.73: 1006
        3.73 -     5.60: 287
        5.60 -     7.47: 21
        7.47 -     9.34: 21
  Bond angle restraints: 5579
  Sorted by residual:
  angle pdb=" C   LYS E 321 "
        pdb=" CA  LYS E 321 "
        pdb=" CB  LYS E 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.87   -9.34 1.65e+00 3.67e-01 3.20e+01
  angle pdb=" C   LYS B 321 "
        pdb=" CA  LYS B 321 "
        pdb=" CB  LYS B 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.85   -9.32 1.65e+00 3.67e-01 3.19e+01
  angle pdb=" C   LYS F 321 "
        pdb=" CA  LYS F 321 "
        pdb=" CB  LYS F 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.85   -9.32 1.65e+00 3.67e-01 3.19e+01
  angle pdb=" C   LYS D 321 "
        pdb=" CA  LYS D 321 "
        pdb=" CB  LYS D 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.85   -9.32 1.65e+00 3.67e-01 3.19e+01
  angle pdb=" C   LYS A 321 "
        pdb=" CA  LYS A 321 "
        pdb=" CB  LYS A 321 "
      ideal   model   delta    sigma   weight residual
     109.53  118.84   -9.31 1.65e+00 3.67e-01 3.19e+01
  ... (remaining 5574 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    12.37: 2058
       12.37 -    24.74: 301
       24.74 -    37.10: 98
       37.10 -    49.47: 49
       49.47 -    61.84: 35
  Dihedral angle restraints: 2541
    sinusoidal: 1064
      harmonic: 1477
  Sorted by residual:
  dihedral pdb=" CA  VAL E 318 "
           pdb=" C   VAL E 318 "
           pdb=" N   THR E 319 "
           pdb=" CA  THR E 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.72  -35.28     0      5.00e+00 4.00e-02 4.98e+01
  dihedral pdb=" CA  VAL G 318 "
           pdb=" C   VAL G 318 "
           pdb=" N   THR G 319 "
           pdb=" CA  THR G 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.73  -35.27     0      5.00e+00 4.00e-02 4.98e+01
  dihedral pdb=" CA  VAL A 318 "
           pdb=" C   VAL A 318 "
           pdb=" N   THR A 319 "
           pdb=" CA  THR A 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.76  -35.24     0      5.00e+00 4.00e-02 4.97e+01
  ... (remaining 2538 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 282
       0.066 -    0.133: 229
       0.133 -    0.199: 63
       0.199 -    0.265: 35
       0.265 -    0.331: 14
  Chirality restraints: 623
  Sorted by residual:
  chirality pdb=" CA  ASP F 348 "
            pdb=" N   ASP F 348 "
            pdb=" C   ASP F 348 "
            pdb=" CB  ASP F 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  ASP E 348 "
            pdb=" N   ASP E 348 "
            pdb=" C   ASP E 348 "
            pdb=" CB  ASP E 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" CA  ASP G 348 "
            pdb=" N   ASP G 348 "
            pdb=" C   ASP G 348 "
            pdb=" CB  ASP G 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.72e+00
  ... (remaining 620 not shown)

  Planarity restraints: 714
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 331 "   -0.016 2.00e-02 2.50e+03   3.07e-02 9.40e+00
        pdb=" C   LYS E 331 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LYS E 331 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PRO E 332 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS G 331 "    0.016 2.00e-02 2.50e+03   3.06e-02 9.39e+00
        pdb=" C   LYS G 331 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LYS G 331 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO G 332 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 331 "    0.016 2.00e-02 2.50e+03   3.06e-02 9.34e+00
        pdb=" C   LYS D 331 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LYS D 331 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO D 332 "    0.018 2.00e-02 2.50e+03
  ... (remaining 711 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1330
        2.90 -     3.40: 3897
        3.40 -     3.90: 6454
        3.90 -     4.40: 6775
        4.40 -     4.90: 14122
  Nonbonded interactions: 32578
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 353 "
            pdb=" OD2 ASP B 358 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" NZ  LYS C 353 "
            pdb=" OD2 ASP C 358 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" NZ  LYS E 353 "
            pdb=" OD2 ASP E 358 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" NZ  LYS A 353 "
            pdb=" OD2 ASP A 358 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" NZ  LYS G 353 "
            pdb=" OD2 ASP G 358 "
     model   vdw
     2.401 3.120
  ... (remaining 32573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.130
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.034   4172  Z= 0.543
  Angle     :  1.799   9.336   5579  Z= 1.104
  Chirality :  0.107   0.331    623
  Planarity :  0.012   0.081    714
  Dihedral  : 16.482  61.835   1603
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  :  8.96 %
    Favored  : 86.57 %
  Cbeta Deviations :  1.49 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.06 (0.19), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.14), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.003   ARG C 349 
 TYR   0.014   0.006   TYR C 310 
 PHE   0.024   0.008   PHE G 346 
 HIS   0.005   0.002   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00816 ( 4172)
  covalent geometry    : angle       1.79867 ( 5579)
  hydrogen bonds       : bond        0.15005 (   95)
  hydrogen bonds       : angle       7.70411 (  285)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  305 SER cc_start: 0.8851 (p) cc_final: 0.8301 (p)
REVERT: A  307 GLN cc_start: 0.8799 (mt0) cc_final: 0.8352 (mp10)
REVERT: A  317 LYS cc_start: 0.7707 (ptmt) cc_final: 0.7347 (ptpp)
REVERT: A  321 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8077 (mttp)
REVERT: A  342 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8267 (mm-30)
REVERT: A  347 LYS cc_start: 0.8597 (tttt) cc_final: 0.8290 (mtpt)
REVERT: B  307 GLN cc_start: 0.8680 (mt0) cc_final: 0.8462 (mp10)
REVERT: B  317 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7589 (ptpp)
REVERT: B  321 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8143 (mttm)
REVERT: B  347 LYS cc_start: 0.8481 (tttt) cc_final: 0.8168 (mtpt)
REVERT: B  369 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8773 (ptpp)
REVERT: C  305 SER cc_start: 0.8744 (p) cc_final: 0.8195 (p)
REVERT: C  307 GLN cc_start: 0.8748 (mt0) cc_final: 0.8358 (mp10)
REVERT: C  317 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7425 (ptpp)
REVERT: C  342 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8296 (mm-30)
REVERT: C  347 LYS cc_start: 0.8334 (tttt) cc_final: 0.8093 (mtpt)
REVERT: D  307 GLN cc_start: 0.9169 (mt0) cc_final: 0.8858 (tm-30)
REVERT: D  317 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7901 (ptpp)
REVERT: D  321 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8330 (mttp)
REVERT: D  342 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7948 (pm20)
REVERT: D  347 LYS cc_start: 0.8705 (tttt) cc_final: 0.8462 (mtpt)
REVERT: E  305 SER cc_start: 0.8822 (p) cc_final: 0.8476 (p)
REVERT: E  307 GLN cc_start: 0.8776 (mt0) cc_final: 0.8348 (tm-30)
REVERT: E  317 LYS cc_start: 0.7736 (ptmt) cc_final: 0.7481 (ptpp)
REVERT: E  321 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8104 (mttp)
REVERT: E  342 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8353 (mm-30)
REVERT: E  347 LYS cc_start: 0.8597 (tttt) cc_final: 0.8276 (mtpt)
REVERT: F  305 SER cc_start: 0.9146 (p) cc_final: 0.8701 (p)
REVERT: F  307 GLN cc_start: 0.9000 (mt0) cc_final: 0.8795 (mp10)
REVERT: F  317 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7973 (ptpp)
REVERT: F  338 GLU cc_start: 0.8259 (tt0) cc_final: 0.8020 (mt-10)
REVERT: F  342 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7993 (pm20)
REVERT: G  305 SER cc_start: 0.8590 (p) cc_final: 0.7920 (p)
REVERT: G  307 GLN cc_start: 0.8662 (mt0) cc_final: 0.8446 (mp10)
REVERT: G  317 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7710 (ptpp)
REVERT: G  369 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8604 (ptpp)
  outliers start: 21
  outliers final: 4
  residues processed: 135
  average time/residue: 0.1304
  time to fit residues: 19.9553
Evaluate side-chains
  68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  373 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 GLN
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 GLN
C 330 HIS
C 351 GLN
D 330 HIS
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 351 GLN
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 351 GLN
G 330 HIS
G 351 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.115857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.097028 restraints weight = 7071.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 3.51
r_work: 0.3891 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4172  Z= 0.123
  Angle     :  0.683   7.919   5579  Z= 0.329
  Chirality :  0.049   0.130    623
  Planarity :  0.003   0.019    714
  Dihedral  :  5.711  17.156    557
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 13.65 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.15 (0.23), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.18), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 349 
 TYR   0.008   0.002   TYR A 310 
 PHE   0.011   0.002   PHE E 378 
 HIS   0.001   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4172)
  covalent geometry    : angle       0.68314 ( 5579)
  hydrogen bonds       : bond        0.02424 (   95)
  hydrogen bonds       : angle       5.43559 (  285)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.7977 (mt0) cc_final: 0.7504 (tm-30)
REVERT: A  344 LEU cc_start: 0.8694 (mp) cc_final: 0.8478 (mp)
REVERT: B  307 GLN cc_start: 0.8035 (mt0) cc_final: 0.7745 (mp10)
REVERT: B  342 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6955 (mm-30)
REVERT: D  307 GLN cc_start: 0.8773 (mt0) cc_final: 0.8567 (tm-30)
REVERT: D  311 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8774 (mtpt)
REVERT: D  342 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7559 (pm20)
REVERT: E  305 SER cc_start: 0.8876 (p) cc_final: 0.8601 (p)
REVERT: E  307 GLN cc_start: 0.8103 (mt0) cc_final: 0.7759 (tm-30)
REVERT: E  338 GLU cc_start: 0.7583 (tt0) cc_final: 0.6742 (mt-10)
REVERT: E  342 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7939 (mm-30)
REVERT: F  305 SER cc_start: 0.8899 (p) cc_final: 0.8185 (p)
REVERT: F  307 GLN cc_start: 0.8585 (mt0) cc_final: 0.8265 (mp10)
  outliers start: 1
  outliers final: 1
  residues processed: 71
  average time/residue: 0.0631
  time to fit residues: 5.8357
Evaluate side-chains
  57 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    4.4188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 362 HIS
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 362 HIS
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.102086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.084587 restraints weight = 7498.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 3.48
r_work: 0.3778 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4172  Z= 0.258
  Angle     :  0.701   5.683   5579  Z= 0.358
  Chirality :  0.051   0.121    623
  Planarity :  0.004   0.023    714
  Dihedral  :  5.434  16.852    553
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.51 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.79 (0.25), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.19), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 349 
 TYR   0.006   0.002   TYR G 310 
 PHE   0.010   0.003   PHE E 378 
 HIS   0.006   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 4172)
  covalent geometry    : angle       0.70143 ( 5579)
  hydrogen bonds       : bond        0.02606 (   95)
  hydrogen bonds       : angle       5.08079 (  285)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  307 GLN cc_start: 0.7986 (mt0) cc_final: 0.7582 (mp10)
REVERT: A  371 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (mm)
REVERT: B  307 GLN cc_start: 0.8049 (mt0) cc_final: 0.7796 (mp10)
REVERT: C  307 GLN cc_start: 0.8187 (mt0) cc_final: 0.7860 (mp10)
REVERT: C  311 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (mtpt)
REVERT: C  342 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7209 (mm-30)
REVERT: D  342 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7555 (pm20)
REVERT: E  305 SER cc_start: 0.8941 (p) cc_final: 0.8640 (p)
REVERT: E  347 LYS cc_start: 0.8032 (tttt) cc_final: 0.7534 (mttt)
REVERT: F  305 SER cc_start: 0.8958 (p) cc_final: 0.8257 (p)
REVERT: F  307 GLN cc_start: 0.8562 (mt0) cc_final: 0.8261 (mp10)
REVERT: F  342 GLU cc_start: 0.7745 (mm-30) cc_final: 0.6742 (pm20)
REVERT: G  307 GLN cc_start: 0.8272 (mt0) cc_final: 0.7899 (tm-30)
REVERT: G  342 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6395 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0767
  time to fit residues: 6.1295
Evaluate side-chains
  61 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain G residue  305 SER
Chi-restraints excluded: chain G residue  342 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0870
   chunk 27 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   overall best weight:    1.3764

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 HIS
G 362 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.115045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.096708 restraints weight = 7277.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.4012 rms_B_bonded: 3.53
r_work: 0.3892 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4172  Z= 0.112
  Angle     :  0.598   8.928   5579  Z= 0.289
  Chirality :  0.047   0.123    623
  Planarity :  0.002   0.016    714
  Dihedral  :  4.644  14.671    553
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.58 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.38 (0.27), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 349 
 TYR   0.004   0.001   TYR D 310 
 PHE   0.007   0.001   PHE E 378 
 HIS   0.003   0.000   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4172)
  covalent geometry    : angle       0.59848 ( 5579)
  hydrogen bonds       : bond        0.02025 (   95)
  hydrogen bonds       : angle       4.84975 (  285)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B  307 GLN cc_start: 0.8085 (mt0) cc_final: 0.7884 (mp10)
REVERT: C  342 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7184 (mm-30)
REVERT: D  342 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7581 (pm20)
REVERT: E  347 LYS cc_start: 0.8026 (tttt) cc_final: 0.7623 (mttt)
REVERT: F  342 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6806 (pm20)
REVERT: G  307 GLN cc_start: 0.8262 (mt0) cc_final: 0.7991 (mp10)
REVERT: G  342 GLU cc_start: 0.6588 (mp0) cc_final: 0.6257 (mp0)
REVERT: G  344 LEU cc_start: 0.9053 (mp) cc_final: 0.8789 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 60
  average time/residue: 0.0700
  time to fit residues: 5.3031
Evaluate side-chains
  59 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 HIS
** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.111981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.093722 restraints weight = 7505.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 3.58
r_work: 0.3836 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4172  Z= 0.153
  Angle     :  0.603   7.834   5579  Z= 0.294
  Chirality :  0.048   0.182    623
  Planarity :  0.002   0.017    714
  Dihedral  :  4.614  15.354    553
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.43 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.25 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG G 349 
 TYR   0.004   0.001   TYR F 310 
 PHE   0.006   0.002   PHE E 378 
 HIS   0.003   0.001   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4172)
  covalent geometry    : angle       0.60343 ( 5579)
  hydrogen bonds       : bond        0.01949 (   95)
  hydrogen bonds       : angle       4.79515 (  285)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8066 (tttt) cc_final: 0.7644 (mttp)
REVERT: C  342 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7200 (mm-30)
REVERT: D  342 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7585 (pm20)
REVERT: E  347 LYS cc_start: 0.8046 (tttt) cc_final: 0.7619 (mttt)
REVERT: F  342 GLU cc_start: 0.7876 (mm-30) cc_final: 0.6638 (pm20)
REVERT: G  307 GLN cc_start: 0.8218 (mt0) cc_final: 0.7986 (mp10)
REVERT: G  342 GLU cc_start: 0.6556 (mp0) cc_final: 0.6193 (mp0)
  outliers start: 8
  outliers final: 5
  residues processed: 62
  average time/residue: 0.0680
  time to fit residues: 5.2937
Evaluate side-chains
  62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 10 optimal weight:    0.0770
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    5.8146

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
B 330 HIS
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 330 HIS
F 330 HIS
F 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.098646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.081497 restraints weight = 7945.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 3.47
r_work: 0.3718 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.045   4172  Z= 0.329
  Angle     :  0.759   8.068   5579  Z= 0.386
  Chirality :  0.052   0.170    623
  Planarity :  0.003   0.024    714
  Dihedral  :  5.616  19.698    553
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.43 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.45 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.21), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 379 
 TYR   0.003   0.002   TYR B 310 
 PHE   0.009   0.003   PHE C 378 
 HIS   0.007   0.002   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00756 ( 4172)
  covalent geometry    : angle       0.75949 ( 5579)
  hydrogen bonds       : bond        0.02491 (   95)
  hydrogen bonds       : angle       5.06282 (  285)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  371 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8131 (mm)
REVERT: B  307 GLN cc_start: 0.7544 (mp10) cc_final: 0.7108 (mp10)
REVERT: C  342 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7475 (mm-30)
REVERT: D  342 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7557 (pm20)
REVERT: E  347 LYS cc_start: 0.8144 (tttt) cc_final: 0.7635 (mttt)
REVERT: F  342 GLU cc_start: 0.7905 (mm-30) cc_final: 0.6737 (pm20)
REVERT: G  307 GLN cc_start: 0.8239 (mt0) cc_final: 0.7972 (mp10)
  outliers start: 12
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0707
  time to fit residues: 6.0104
Evaluate side-chains
  67 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0060
   chunk 16 optimal weight:    8.9990
   chunk 41 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 7 optimal weight:   20.0000
   chunk 23 optimal weight:    0.4980
   chunk 29 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   overall best weight:    4.1002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.100837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.083373 restraints weight = 7777.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 3.51
r_work: 0.3750 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4172  Z= 0.240
  Angle     :  0.687   8.780   5579  Z= 0.339
  Chirality :  0.049   0.142    623
  Planarity :  0.003   0.016    714
  Dihedral  :  5.309  17.989    553
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.57 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.36 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.002   0.001   TYR E 310 
 PHE   0.007   0.002   PHE E 378 
 HIS   0.005   0.001   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 4172)
  covalent geometry    : angle       0.68711 ( 5579)
  hydrogen bonds       : bond        0.02179 (   95)
  hydrogen bonds       : angle       5.03335 (  285)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7329 (mm-30)
REVERT: B  307 GLN cc_start: 0.7536 (mp10) cc_final: 0.7089 (mp10)
REVERT: C  342 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7557 (mm-30)
REVERT: D  342 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7640 (pm20)
REVERT: E  347 LYS cc_start: 0.8143 (tttt) cc_final: 0.7646 (mttt)
REVERT: F  342 GLU cc_start: 0.7938 (mm-30) cc_final: 0.6654 (pm20)
REVERT: G  307 GLN cc_start: 0.8242 (mt0) cc_final: 0.8039 (mp10)
  outliers start: 10
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0760
  time to fit residues: 6.4148
Evaluate side-chains
  69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0870
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    4.6166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.100109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.082553 restraints weight = 7686.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 3.48
r_work: 0.3737 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4172  Z= 0.267
  Angle     :  0.725   8.893   5579  Z= 0.358
  Chirality :  0.050   0.155    623
  Planarity :  0.003   0.017    714
  Dihedral  :  5.393  18.353    553
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.71 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.35 (0.28), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 379 
 TYR   0.002   0.001   TYR E 310 
 PHE   0.008   0.002   PHE D 378 
 HIS   0.006   0.002   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 4172)
  covalent geometry    : angle       0.72501 ( 5579)
  hydrogen bonds       : bond        0.02223 (   95)
  hydrogen bonds       : angle       5.03565 (  285)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7331 (mm-30)
REVERT: A  371 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8092 (mm)
REVERT: B  307 GLN cc_start: 0.7534 (mp10) cc_final: 0.7099 (mp10)
REVERT: C  342 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7568 (mm-30)
REVERT: D  342 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7634 (pm20)
REVERT: D  380 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6015 (tp30)
REVERT: E  347 LYS cc_start: 0.8161 (tttt) cc_final: 0.7663 (mttt)
REVERT: F  342 GLU cc_start: 0.7956 (mm-30) cc_final: 0.6690 (pm20)
REVERT: G  307 GLN cc_start: 0.8146 (mt0) cc_final: 0.7848 (mp10)
  outliers start: 14
  outliers final: 11
  residues processed: 72
  average time/residue: 0.0721
  time to fit residues: 6.6488
Evaluate side-chains
  76 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0980
   chunk 8 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.104309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.086018 restraints weight = 7490.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 3.55
r_work: 0.3803 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4172  Z= 0.144
  Angle     :  0.651   8.936   5579  Z= 0.312
  Chirality :  0.048   0.134    623
  Planarity :  0.002   0.016    714
  Dihedral  :  4.789  15.364    553
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.14 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.29), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 379 
 TYR   0.002   0.001   TYR F 310 
 PHE   0.005   0.001   PHE E 378 
 HIS   0.003   0.001   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4172)
  covalent geometry    : angle       0.65121 ( 5579)
  hydrogen bonds       : bond        0.01739 (   95)
  hydrogen bonds       : angle       4.77447 (  285)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7364 (mm-30)
REVERT: A  380 GLU cc_start: 0.6757 (tm-30) cc_final: 0.5889 (tp30)
REVERT: B  307 GLN cc_start: 0.7598 (mp10) cc_final: 0.7152 (mp10)
REVERT: B  380 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6598 (tp30)
REVERT: C  342 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7561 (mm-30)
REVERT: D  342 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7666 (pm20)
REVERT: D  380 GLU cc_start: 0.6998 (tm-30) cc_final: 0.5973 (tp30)
REVERT: E  347 LYS cc_start: 0.8145 (tttt) cc_final: 0.7692 (mttt)
REVERT: F  342 GLU cc_start: 0.7969 (mm-30) cc_final: 0.6635 (pm20)
REVERT: G  307 GLN cc_start: 0.8116 (mt0) cc_final: 0.7777 (mp10)
  outliers start: 12
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0575
  time to fit residues: 5.5276
Evaluate side-chains
  75 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.104299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.086188 restraints weight = 7384.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 3.50
r_work: 0.3808 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4172  Z= 0.157
  Angle     :  0.665   8.771   5579  Z= 0.318
  Chirality :  0.048   0.133    623
  Planarity :  0.002   0.020    714
  Dihedral  :  4.640  15.075    553
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.20 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.13 (0.30), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.002   0.001   TYR E 310 
 PHE   0.005   0.001   PHE E 378 
 HIS   0.003   0.001   HIS G 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4172)
  covalent geometry    : angle       0.66513 ( 5579)
  hydrogen bonds       : bond        0.01693 (   95)
  hydrogen bonds       : angle       4.72214 (  285)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1050 Ramachandran restraints generated.
    525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  342 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: B  307 GLN cc_start: 0.7611 (mp10) cc_final: 0.7165 (mp10)
REVERT: C  342 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: D  342 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7664 (pm20)
REVERT: D  380 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6059 (tp30)
REVERT: E  347 LYS cc_start: 0.8205 (tttt) cc_final: 0.7732 (mttt)
REVERT: F  342 GLU cc_start: 0.7977 (mm-30) cc_final: 0.6665 (pm20)
REVERT: G  307 GLN cc_start: 0.8196 (mt0) cc_final: 0.7844 (mp10)
  outliers start: 12
  outliers final: 12
  residues processed: 72
  average time/residue: 0.0658
  time to fit residues: 6.1441
Evaluate side-chains
  78 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain C residue  305 SER
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain D residue  305 SER
Chi-restraints excluded: chain D residue  356 SER
Chi-restraints excluded: chain D residue  373 THR
Chi-restraints excluded: chain E residue  305 SER
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain F residue  305 SER
Chi-restraints excluded: chain G residue  305 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0270
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    4.6046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.100278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.082400 restraints weight = 7675.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 3.51
r_work: 0.3734 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   4172  Z= 0.264
  Angle     :  0.745   9.018   5579  Z= 0.363
  Chirality :  0.050   0.142    623
  Planarity :  0.003   0.016    714
  Dihedral  :  5.133  17.594    553
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.20 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.29), residues: 525
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 379 
 TYR   0.003   0.001   TYR E 310 
 PHE   0.007   0.002   PHE C 378 
 HIS   0.006   0.002   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 4172)
  covalent geometry    : angle       0.74451 ( 5579)
  hydrogen bonds       : bond        0.02149 (   95)
  hydrogen bonds       : angle       4.91596 (  285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1148.66 seconds
wall clock time: 20 minutes 41.49 seconds (1241.49 seconds total)